Studying enzyme enantioselectivity using combined ab initio and free energy calculations: α-chymotrypsin and methyl cis- and trans-5-oxo-2-pentylpirrolidine-3-carboxylates

Abstract

The application of a computational approach, based on molecular dynamics (MD) simulations and quantum mechanical-free energy (QM-FE) calculations, to explain the different substrate specificity and enantioselectivity of α-chymotrypsin (α-CT) in the hydrolysis of methyl cis- and trans-5-oxo-2-pentylpirrolidine-3-carboxylates is described. By applying a combination of molecular mechanics energy derived from MD simulations in explicit solvent, and solvation free energy derived from a continuum solvation model, we have calculated reasonable absolute free energies of binding (Δ G bind) for each α-CT/enantiomer complex formation, and elucidated the balanced nature of the factors contributing to Δ G bind. Furthermore, our calculations based on QM-FE techniques have yielded an insight into the major issues affecting the observed enantioselectivity in the hydrolysis of substrate ester bonds by α-chymotrypsin.